Re: [AMBER] Using custom non-bonding potential, drude oscillator in Amber18

From: David A Case <>
Date: Tue, 16 Oct 2018 09:22:43 -0400

On Mon, Oct 15, 2018, Kyeong-jun Jeong wrote:
> I would like to use a custom non-bonding potential which does not fit to
> LJ 12-6 terms in Hamiltonian, and also drude oscillators for explicit
> polarization.
> Is there any way to implement those in the Amber software, especially in
> pmemd if possible?

If the non-bonded exclusions and lists would be unchanged, it's probably
not too hard to change the functional form. But note that you would
have to also write code to get any parameters you need into the right
places: LJ terms (out of the box) depend heavily on "mixing rules" to
establish all of the parameters for different pairs of atoms types.

You might want to look at openMM: its design is much friendlier to
including custom potentials (and its GPU performance it reported to be
pretty good, although I don't have any recent personal experience.)
> Is it possible to either change the Hamiltonian or import tabulated
> potential? Also, are drude oscillators and the dual thermostat for those
> supported?

This is not (yet?) supported in Amber. There is a DrudeForce class in
openMM; again, I have no personal experience with it.

...good luck....dac

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Received on Tue Oct 16 2018 - 06:30:03 PDT
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